Bash - Copy files iteratively - bash

Question

I want to copy a list of files, called dti_fin_fa, from one folder to another.
These files are scattered in different folders.
Controls
└───C01
│ └───difusion
│ └───Deterministic
│ └───dti_fin_fa.nii
└───C02
│ └───difusion
│ └───Deterministic
│ └───dti_fin_fa.nii
└───C03
│ └───difusion
│ └───Deterministic
│ └───dti_fin_fa.nii
I want to select and copy all the dti_fin_fa, keeping the folder structure, so, in my new directory, I would have the folder distribution just seen above. The problem is that in this folders, (deterministic, difusion, etc), there are lots of other files I don´t want to copy, so I can´t just copy the main folder (C01 etc)
This is what I have:
#!/bin/bash
DIR="/media/Batty/Analysis"; cd "$DIR" || exit
for group in Controls; do
for folder in $group/*; do
for dti in $folder/difussion/Deterministic/dti_fin_fa.nii; do
echo $dti
cp $dti /media/Roy/Analysis/Controls/ --verbose
done;
done;
done;
The problem is that this code copies each of the dti_fin_fa.nii images into /media/Roy/Analysis/Controls/, hence keeping just the last one, instead of creating all the other subfolders.
Could something like this work?
cp $folder/difusion/Deterministic/$dti /media/Roy/Analysis/Patients/ --verbose

Answer 1

Iterate through each control, make the equivalent directory and copy only the file you want:
for group in "Control"/* "Patients"/*; do
orig="$group/difusion/Deterministic"
dest="/media/Roy/Analysis/Controls/$(dirname group)/$orig"
mkdir -p "$dest"
cp "$orig/dti_fin_fa.nii" "$dest/"
done
I suppose you execute this from the DIR directory of your example. So here orig is the relative path to the image folder, dest is the absolute path to your destination directory, including the preserved original folder structure. mkdir -p ensures that such end directory exists and finally the image is copied.